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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.7

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

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        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2019-02-21, 17:26 based on data in: /common/bermanblab/data/public_data/ENCODE/SNYDER_CRISPRi/ALIGNMENT


        General Statistics

        Showing 171/171 rows and 6/6 columns.
        Sample Name% AssignedM Assigned% rRNA% mRNA% AlignedM Aligned
        ENCSR000CPH_1
        61.3%
        163.1
        0.0%
        83.6%
        83.5%
        94.9
        ENCSR000CPH_2
        60.2%
        168.6
        0.0%
        82.6%
        83.1%
        98.9
        ENCSR011GAO_1
        42.8%
        34.1
        0.0%
        63.7%
        79.0%
        25.4
        ENCSR011GAO_2
        54.7%
        59.0
        0.0%
        82.1%
        81.7%
        34.0
        ENCSR016WFQ_1
        60.3%
        62.8
        0.0%
        81.8%
        82.0%
        37.3
        ENCSR016WFQ_2
        50.8%
        41.8
        0.0%
        74.4%
        79.7%
        26.8
        ENCSR024HAR_1
        54.0%
        53.4
        0.0%
        90.3%
        67.4%
        28.5
        ENCSR024HAR_2
        53.0%
        34.7
        0.0%
        85.4%
        69.5%
        19.7
        ENCSR028FBD_1
        48.6%
        48.1
        0.0%
        90.1%
        59.1%
        25.8
        ENCSR028FBD_2
        46.4%
        42.5
        0.0%
        88.7%
        58.9%
        22.9
        ENCSR039VEQ_1
        55.9%
        41.2
        0.0%
        82.2%
        79.5%
        24.0
        ENCSR039VEQ_3
        48.8%
        47.8
        0.0%
        85.1%
        65.2%
        26.9
        ENCSR039VEQ_4
        46.7%
        45.2
        0.0%
        85.1%
        62.4%
        25.3
        ENCSR043UMW_3
        45.5%
        43.2
        0.0%
        75.1%
        68.7%
        27.6
        ENCSR043UMW_4
        42.4%
        48.1
        0.0%
        72.3%
        66.3%
        31.9
        ENCSR046FQX_1
        49.5%
        47.0
        0.0%
        85.6%
        64.8%
        26.5
        ENCSR046FQX_2
        47.3%
        46.0
        0.0%
        84.7%
        64.2%
        25.9
        ENCSR052BWT_1
        47.6%
        35.0
        0.0%
        64.5%
        82.9%
        25.9
        ENCSR052BWT_2
        32.4%
        48.1
        76.2%
        36.5
        ENCSR052ZPX_3
        56.6%
        51.8
        0.0%
        88.6%
        72.8%
        28.1
        ENCSR052ZPX_4
        54.0%
        46.8
        0.0%
        88.1%
        68.8%
        25.6
        ENCSR069OUL_1
        47.5%
        46.9
        0.0%
        73.2%
        79.7%
        30.3
        ENCSR069OUL_2
        54.7%
        58.1
        0.0%
        76.0%
        84.2%
        36.7
        ENCSR073QLQ_1
        35.1%
        37.1
        0.0%
        89.1%
        42.3%
        20.0
        ENCSR073QLQ_2
        43.0%
        45.2
        0.0%
        83.3%
        59.6%
        25.8
        ENCSR074FBG_1
        34.7%
        41.4
        0.0%
        81.5%
        51.5%
        23.1
        ENCSR074FBG_2
        32.9%
        42.4
        0.0%
        81.7%
        51.4%
        23.0
        ENCSR084NTT_1
        62.4%
        79.9
        0.0%
        87.6%
        82.4%
        43.8
        ENCSR084NTT_2
        61.4%
        64.0
        0.0%
        86.3%
        82.2%
        35.6
        ENCSR095PIC_1
        51.5%
        32.0
        0.0%
        86.6%
        65.3%
        17.9
        ENCSR095PIC_2
        57.5%
        52.1
        0.0%
        90.8%
        71.4%
        27.7
        ENCSR096VPS_3
        36.9%
        35.5
        0.0%
        72.1%
        57.6%
        23.5
        ENCSR096VPS_4
        36.6%
        25.4
        0.0%
        59.4%
        68.5%
        20.5
        ENCSR103URL_1
        61.9%
        43.2
        0.0%
        90.0%
        80.3%
        23.1
        ENCSR103URL_2
        57.9%
        62.3
        0.0%
        88.3%
        78.8%
        33.4
        ENCSR104JMN_1
        50.7%
        53.2
        0.0%
        85.7%
        64.6%
        30.2
        ENCSR104JMN_2
        43.0%
        41.1
        0.0%
        79.7%
        58.3%
        25.0
        ENCSR104QKG_3
        36.3%
        25.2
        0.0%
        80.5%
        55.6%
        14.2
        ENCSR104QKG_4
        38.1%
        32.7
        0.0%
        81.5%
        56.5%
        18.5
        ENCSR123IMQ_1
        46.7%
        31.0
        0.0%
        88.3%
        58.9%
        16.8
        ENCSR123IMQ_2
        56.0%
        40.8
        0.0%
        88.6%
        70.9%
        22.2
        ENCSR126GEQ_1
        32.0%
        42.4
        0.0%
        86.6%
        40.4%
        23.1
        ENCSR126GEQ_2
        31.8%
        35.1
        0.0%
        82.0%
        46.1%
        19.5
        ENCSR160YSN_1
        44.4%
        12.5
        0.0%
        64.6%
        78.2%
        9.3
        ENCSR160YSN_2
        35.3%
        62.0
        0.0%
        82.4%
        46.6%
        35.8
        ENCSR171KMM_1
        43.7%
        46.4
        0.0%
        71.6%
        80.2%
        30.0
        ENCSR171KMM_2
        53.1%
        46.2
        0.0%
        83.7%
        71.9%
        26.5
        ENCSR171KMM_3
        47.8%
        48.3
        0.0%
        79.8%
        67.0%
        29.2
        ENCSR171KMM_4
        46.5%
        66.1
        0.0%
        81.5%
        65.1%
        38.7
        ENCSR171RTN_1
        49.2%
        48.2
        0.0%
        86.4%
        68.3%
        26.2
        ENCSR171RTN_2
        33.8%
        42.9
        0.0%
        82.6%
        52.0%
        23.1
        ENCSR181WYS_1
        41.8%
        51.1
        0.0%
        75.7%
        77.0%
        30.5
        ENCSR181WYS_2
        53.8%
        54.2
        0.0%
        81.3%
        78.2%
        31.7
        ENCSR181WYS_3
        43.9%
        44.0
        0.0%
        78.9%
        63.8%
        26.5
        ENCSR181WYS_4
        53.4%
        44.8
        0.0%
        86.6%
        73.1%
        24.5
        ENCSR184VVN_1
        57.5%
        56.5
        0.0%
        82.3%
        80.2%
        33.0
        ENCSR184VVN_2
        56.1%
        69.5
        0.0%
        82.4%
        77.8%
        40.5
        ENCSR190RZZ_1
        49.6%
        31.3
        0.0%
        85.3%
        65.3%
        17.7
        ENCSR190RZZ_2
        47.0%
        39.4
        0.0%
        79.6%
        67.7%
        23.7
        ENCSR200UDS_1
        41.9%
        36.0
        0.0%
        81.5%
        55.7%
        21.3
        ENCSR200UDS_2
        48.7%
        38.3
        0.0%
        88.2%
        60.5%
        21.1
        ENCSR223QTD_1
        43.7%
        37.1
        0.0%
        60.4%
        82.6%
        29.5
        ENCSR223QTD_2
        34.4%
        42.8
        0.0%
        70.0%
        73.2%
        26.8
        ENCSR235ZEI_1
        58.2%
        54.7
        0.0%
        85.9%
        77.2%
        30.6
        ENCSR235ZEI_3
        50.8%
        57.4
        0.0%
        89.0%
        65.2%
        30.7
        ENCSR235ZEI_4
        55.4%
        56.9
        0.0%
        85.6%
        74.6%
        31.8
        ENCSR243VNX_1
        38.7%
        31.7
        0.0%
        60.6%
        79.3%
        24.6
        ENCSR243VNX_2
        61.3%
        47.6
        0.0%
        89.3%
        79.7%
        25.6
        ENCSR263IOO_1
        53.4%
        45.0
        0.0%
        76.8%
        80.0%
        28.2
        ENCSR263IOO_2
        57.3%
        52.8
        0.0%
        84.4%
        80.1%
        29.9
        ENCSR267BHU_1
        50.1%
        43.2
        0.0%
        83.0%
        66.1%
        25.2
        ENCSR267BHU_2
        49.1%
        73.9
        0.0%
        87.8%
        61.0%
        40.8
        ENCSR268DNJ_1
        36.5%
        45.6
        43.2%
        24.7
        ENCSR268DNJ_2
        39.3%
        27.4
        0.0%
        86.4%
        49.1%
        15.1
        ENCSR294ZCD_1
        31.8%
        32.2
        0.0%
        79.5%
        51.1%
        17.9
        ENCSR294ZCD_2
        38.3%
        30.3
        0.0%
        82.6%
        56.8%
        16.8
        ENCSR299HUJ_1
        62.0%
        54.8
        0.0%
        87.7%
        81.9%
        30.1
        ENCSR299HUJ_3
        46.3%
        38.2
        0.0%
        85.1%
        64.8%
        21.0
        ENCSR299HUJ_4
        50.7%
        65.9
        0.0%
        84.3%
        70.6%
        37.1
        ENCSR357LVC_3
        41.8%
        40.0
        0.0%
        67.0%
        70.3%
        28.7
        ENCSR357LVC_4
        48.7%
        45.0
        0.0%
        87.9%
        65.3%
        24.1
        ENCSR359VJC_1
        11.1%
        18.9
        0.1%
        52.9%
        32.7%
        10.4
        ENCSR359VJC_2
        6.7%
        16.6
        0.2%
        40.3%
        24.3%
        9.3
        ENCSR369BHC_1
        40.5%
        29.0
        0.0%
        64.3%
        79.9%
        21.1
        ENCSR369BHC_2
        57.0%
        60.7
        0.0%
        86.2%
        80.4%
        33.4
        ENCSR376CFR_1
        28.6%
        53.9
        0.0%
        75.0%
        54.1%
        30.4
        ENCSR376CFR_2
        43.4%
        47.5
        0.0%
        81.8%
        58.8%
        27.9
        ENCSR381TNV_1
        45.7%
        29.9
        0.0%
        88.7%
        57.8%
        16.1
        ENCSR381TNV_2
        50.2%
        22.6
        0.0%
        89.3%
        62.6%
        12.2
        ENCSR385ZTW_1
        48.3%
        54.6
        0.0%
        72.7%
        81.3%
        35.5
        ENCSR385ZTW_2
        53.8%
        47.6
        0.0%
        77.7%
        80.0%
        29.5
        ENCSR385ZTW_3
        40.1%
        36.5
        0.0%
        62.3%
        72.3%
        28.1
        ENCSR385ZTW_4
        41.6%
        36.4
        0.0%
        67.1%
        69.6%
        26.0
        ENCSR389OCD_1
        43.7%
        43.7
        0.0%
        86.1%
        55.0%
        24.6
        ENCSR389OCD_2
        44.3%
        39.7
        0.0%
        91.3%
        52.4%
        21.0
        ENCSR399QAP_1
        49.8%
        65.9
        0.0%
        82.3%
        68.4%
        38.6
        ENCSR399QAP_2
        51.9%
        54.7
        0.0%
        78.3%
        73.3%
        33.9
        ENCSR409OFU_1
        7.6%
        23.5
        0.3%
        42.3%
        29.4%
        13.1
        ENCSR409OFU_2
        3.9%
        17.5
        0.4%
        27.9%
        18.9%
        10.3
        ENCSR469EFL_1
        23.9%
        34.8
        0.1%
        76.9%
        39.7%
        19.0
        ENCSR469EFL_2
        29.6%
        34.0
        0.0%
        80.3%
        46.0%
        18.7
        ENCSR545HTM_1
        56.9%
        76.1
        0.0%
        77.5%
        84.1%
        47.5
        ENCSR545HTM_2
        52.4%
        59.5
        0.0%
        86.6%
        77.9%
        31.9
        ENCSR550FIL_1
        30.2%
        37.6
        0.0%
        79.5%
        49.1%
        20.6
        ENCSR550FIL_2
        46.5%
        29.1
        0.0%
        88.5%
        58.5%
        15.7
        ENCSR552HTC_1
        29.1%
        46.8
        0.0%
        86.9%
        35.7%
        25.3
        ENCSR552HTC_2
        30.5%
        56.7
        0.0%
        84.4%
        41.0%
        30.5
        ENCSR557BMX_1
        45.2%
        34.3
        0.0%
        82.7%
        59.3%
        20.1
        ENCSR557BMX_2
        40.7%
        37.1
        0.0%
        89.5%
        49.2%
        20.0
        ENCSR591QYK_1
        40.6%
        34.9
        0.0%
        85.7%
        54.1%
        19.2
        ENCSR591QYK_2
        30.1%
        32.7
        0.0%
        77.6%
        49.5%
        18.5
        ENCSR608ORR_1
        56.3%
        72.2
        0.0%
        86.3%
        79.3%
        39.7
        ENCSR608ORR_2
        39.3%
        43.7
        0.0%
        78.5%
        72.9%
        24.5
        ENCSR619EYC_1
        30.0%
        23.8
        0.0%
        81.1%
        42.1%
        13.6
        ENCSR619EYC_2
        35.5%
        32.6
        0.0%
        85.7%
        46.0%
        18.0
        ENCSR620DOP_1
        43.9%
        47.2
        0.0%
        86.8%
        62.0%
        25.3
        ENCSR620DOP_2
        50.9%
        50.6
        0.0%
        88.4%
        63.3%
        27.7
        ENCSR650QAK_1
        51.0%
        29.5
        0.0%
        86.3%
        67.9%
        16.3
        ENCSR650QAK_3
        41.4%
        65.2
        0.0%
        82.2%
        58.4%
        37.3
        ENCSR650QAK_4
        37.4%
        59.5
        0.0%
        82.3%
        58.9%
        32.3
        ENCSR688UTN_1
        49.9%
        40.2
        0.0%
        78.5%
        75.2%
        24.3
        ENCSR688UTN_3
        49.0%
        45.9
        0.0%
        88.0%
        64.1%
        24.8
        ENCSR688UTN_4
        52.5%
        50.2
        0.0%
        89.1%
        67.8%
        26.9
        ENCSR701TVL_1
        53.1%
        52.5
        0.0%
        83.4%
        70.0%
        30.6
        ENCSR701TVL_2
        57.7%
        81.5
        0.0%
        83.7%
        75.9%
        47.5
        ENCSR713AEC_1
        46.3%
        41.6
        0.0%
        67.5%
        80.1%
        29.5
        ENCSR713AEC_2
        43.2%
        40.6
        0.0%
        61.1%
        82.1%
        31.8
        ENCSR715EDZ_2
        53.5%
        42.0
        0.0%
        83.4%
        75.5%
        23.9
        ENCSR715EDZ_3
        34.7%
        47.5
        0.0%
        83.8%
        46.0%
        26.6
        ENCSR715EDZ_4
        41.3%
        69.6
        0.0%
        79.9%
        60.1%
        40.9
        ENCSR731FEO_3
        43.9%
        32.9
        0.0%
        84.6%
        61.0%
        18.2
        ENCSR731FEO_4
        33.1%
        42.0
        0.0%
        78.8%
        57.5%
        23.1
        ENCSR731XIE_1
        28.0%
        33.9
        0.0%
        85.5%
        35.5%
        18.6
        ENCSR731XIE_2
        29.5%
        34.8
        0.0%
        78.9%
        46.9%
        19.4
        ENCSR733ROU_1
        32.4%
        32.7
        0.0%
        88.0%
        40.0%
        17.6
        ENCSR733ROU_2
        32.0%
        41.7
        0.0%
        87.3%
        39.6%
        22.7
        ENCSR733TFF_1
        50.7%
        35.0
        0.0%
        85.3%
        66.3%
        19.8
        ENCSR733TFF_2
        33.5%
        22.1
        0.0%
        81.2%
        44.2%
        13.1
        ENCSR734VBC_1
        36.2%
        50.6
        0.0%
        86.9%
        47.4%
        27.3
        ENCSR734VBC_2
        30.3%
        30.9
        0.0%
        86.9%
        38.0%
        16.7
        ENCSR761AQZ_1
        7.0%
        27.0
        0.2%
        40.9%
        25.2%
        15.3
        ENCSR761AQZ_2
        5.8%
        23.3
        0.3%
        36.6%
        23.5%
        13.5
        ENCSR773VKE_1
        47.3%
        43.2
        0.0%
        84.8%
        61.4%
        24.6
        ENCSR773VKE_2
        41.0%
        76.5
        0.0%
        85.8%
        51.8%
        43.0
        ENCSR781XJD_1
        47.8%
        50.2
        0.0%
        69.1%
        80.7%
        34.9
        ENCSR781XJD_2
        47.8%
        55.7
        0.0%
        80.9%
        76.7%
        31.7
        ENCSR800PWS_1
        24.9%
        37.6
        0.0%
        80.0%
        36.0%
        20.8
        ENCSR800PWS_2
        42.2%
        29.3
        0.0%
        87.5%
        55.0%
        15.8
        ENCSR808HQN_1
        50.0%
        66.0
        0.0%
        80.6%
        77.3%
        38.4
        ENCSR808HQN_3
        37.9%
        38.7
        0.0%
        86.7%
        48.7%
        21.0
        ENCSR808HQN_4
        43.7%
        46.9
        0.0%
        86.7%
        58.1%
        25.4
        ENCSR810RIC_1
        56.2%
        36.1
        0.0%
        82.0%
        79.4%
        21.2
        ENCSR810RIC_2
        30.9%
        50.8
        0.0%
        71.9%
        70.7%
        29.3
        ENCSR819PCU_1
        57.6%
        60.8
        0.0%
        87.6%
        77.6%
        33.1
        ENCSR819PCU_2
        40.4%
        25.6
        0.0%
        86.8%
        53.0%
        13.8
        ENCSR819PCU_3
        41.6%
        29.3
        0.0%
        85.4%
        54.9%
        16.3
        ENCSR850LOZ_1
        53.9%
        57.8
        0.0%
        85.3%
        78.6%
        31.7
        ENCSR850LOZ_2
        51.6%
        73.5
        0.0%
        80.8%
        79.2%
        42.7
        ENCSR862UHT_1
        53.1%
        63.6
        0.0%
        87.0%
        67.5%
        35.5
        ENCSR862UHT_2
        51.2%
        33.3
        0.0%
        83.9%
        66.7%
        19.3
        ENCSR898UNK_1
        41.9%
        46.2
        0.0%
        82.4%
        57.6%
        26.7
        ENCSR898UNK_2
        37.1%
        48.3
        0.0%
        84.2%
        51.3%
        26.7
        ENCSR900AQL_1
        59.5%
        53.4
        0.0%
        84.9%
        76.5%
        30.6
        ENCSR900AQL_2
        65.4%
        58.0
        0.0%
        87.3%
        80.7%
        32.6
        ENCSR905SEH_1
        32.3%
        30.0
        0.0%
        85.5%
        43.9%
        16.1
        ENCSR905SEH_2
        37.7%
        31.5
        0.0%
        84.9%
        52.6%
        17.2
        ENCSR911BML_1
        57.8%
        72.1
        0.0%
        88.3%
        79.5%
        38.7
        ENCSR911BML_2
        26.0%
        43.0
        0.0%
        67.1%
        63.1%
        25.8
        ENCSR942XXL_1
        44.8%
        38.9
        0.0%
        65.6%
        80.0%
        28.3
        ENCSR942XXL_2
        45.9%
        59.1
        0.0%
        83.0%
        75.7%
        32.2
        FAIL_EXAMPLE
        0.0%
        0.0
        0.0%
        29.3%
        0.0%
        0.0

        Preseq

        Preseq estimates the complexity of a library, showing how many additional unique reads are sequenced for increasing total read count. A shallow curve indicates complexity saturation. The dashed line shows a perfectly complex library where total reads = unique reads.

        Complexity curve

        Note that the x axis is trimmed at the point where all the datasets show 80% of their maximum y-value, to avoid ridiculous scales.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        RnaSeqMetrics Assignment

        Number of bases in primary alignments that align to regions in the reference genome.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        RnaSeqMetrics Strand Mapping

        Number of aligned reads that map to the correct strand.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Gene Coverage

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).